Hey Evan, Out of curiosity, are you trying to update MSI's CLIA pipeline to utilize tool shed installed tools? (It sounds kind of like yes.) I don't think that file you mentioned exists in either place - is it a typo or maybe a configuration file with overridden location in universe_wsgi.ini? Reading between the lines, it sounds like you want Galaxy cloud images with completely fresh Galaxy instances but with preinstalled tools? There are many variants of the following approach that I think could work - but one approach is: Create a persistent directory (...or at least a directory that can be recreated when you launch a new VM) like: /mnt/gx_tools It should have the following contents: shed_tools/ (empty directory) shed_tool_conf.xml (contents like <toolbox tool_path="/mnt/gx_tools/shed_tools"></toolbox>). dependencies/ (empty directory) Now create a throw away Galaxy instance and update its universe_wsgi.ini with the following properties: [app:main] tool_dependency_dir = /mnt/gx_tools/dependencies install_database_connection = sqlite:////mnt/gx_tools/install_database.sqlite?isolation_level=IMMEDIATE tool_config_file = tool_conf.xml,/mnt/gx_tools/shed_tool_conf.xml Bootstrap and install tools. Throw away or wipe out Galaxy data and take a snapshot. Now just ensure new Galaxy VM instances starts with the above 3 properties set the same way. Hope this helps. -John On Tue, May 20, 2014 at 3:40 PM, Evan Bollig <boll0107@umn.edu> wrote:
I want to setup a tool_shed_install.xml to roll out tools at first boot for Galaxy.
1) Is it possible to get Galaxy to generate this based on the tools currently installed from the tool shed?
2) Is it required to list every tool provided by each repository, or can I simply add the repository to the file and Galaxy will assume all tools are included?
3) The tool_shed_install.xml.sample file exists only in the galaxy-central#default branch. This should probably be included in the galaxy-dist#stable too.
Cheers,
-Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/